Extremophiles最新文献

{"title":"Long-term heavy metal contamination altered the structure and function of microbial communities in agricultural soil.","authors":"Hongling Liu, Yonghua Zhang, Keke Yang, Huan Li, Susu Cao, Yuanyuan Bao, Lu Feng, Li Zhang, Jingping Niu, Tian Tian","doi":"10.1007/s00792-026-01434-5","DOIUrl":"10.1007/s00792-026-01434-5","url":null,"abstract":"<p><p>Heavy metal (HM) contamination from mining poses a long-term threat to agricultural soils. This study assessed the impacts of long-term HM exposure on soil microbial communities by comparing contaminated and uncontaminated agricultural soils from northwestern China. Using physicochemical analyses and high-throughput amplicon sequencing of bacterial and fungal communities, we assessed impacts on microbial community composition, co-occurrence networks, and predicted functions. HM contamination significantly reduced fungal α-diversity and altered the composition of both bacterial and fungal communities. The relative abundances of Actinobacteria, Acidobacteria, and Chloroflexi increased significantly in contaminated soils. Fungal communities were markedly enriched in Mortierellomycota. Notably, HM contamination substantially reduced the complexity of microbial co-occurrence networks, as indicated by fewer nodes, edges, and keystone taxa. Predictive functional profiling suggested an increased predicted abundance of functions related to HM resistance and detoxification, alongside shifts in core nutrient cycling potentials. Specifically, carbon and nitrogen metabolic pathways were altered, and the proportion of saprotrophic fungi increased, suggesting changes in organic matter decomposition dynamics. In conclusion, long-term HM stress is associated with a shift toward a simplified state, characterized by taxonomic restructuring, less complex co-occurrence networks, and a functional shift toward stress resistance and altered nutrient cycling.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148249944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Decoding the cold: integrated secretome profiling reveals extracellular adaptation mechanisms in Glaciozyma antarctica.","authors":"Shuhaila Mat-Sharani, Farahayu Khairuddin, Nik Yusnoraini Yusof, Norfarhan Mohd-Assaad, Abdul Munir Abdul Murad, Farah Diba Abu Bakar, Nor Muhammad Mahadi, Nurdiana Nordin, Shazilah Kamaruddin","doi":"10.1007/s00792-026-01433-6","DOIUrl":"10.1007/s00792-026-01433-6","url":null,"abstract":"<p><p>Glaciozyma antarctica is an Antarctic psychrophilic yeast providing an excellent eukaryotic model for dissecting molecular mechanisms of cold adaptation. Yet, its extracellular protein repertoire, the interface between the cell and extreme surroundings, remains unexplored. Here, we present the first integrated bioinformatics-proteomics secretome map of G. antarctica, linking computational prediction with experimental validation under varying temperature stress, yielding 9 high-confidence experimentally supported secreted proteins. Three complementary pipelines (Phobius, SignalP/TMHMM, and WoLF PSORT) predicted 278 high-confidence secreted proteins, predominantly glycosyl hydrolases, lipases, oxidoreductases, and stress-response factors. To validate these predictions, we performed LC-MS/MS analysis of extracellular fractions from cultures exposed to - 12 °C, 0 °C, and 12 °C. A total of 104 secreted proteins was identified, including 55 shared across all temperatures and multiple unique cold-induced candidates such as antifreeze proteins and glycosidases. Comparative analysis uncovered a temperature-dependent remodeling of the secretome and revealed several proteins lacking canonical signal peptides, highlighting potential unconventional secretion mechanisms or moonlighting roles in extracellular environments. These findings demonstrate that G. antarctica adapts to freezing environments by dynamically reshaping its extracellular proteome to maintain structural plasticity and metabolic efficiency. This integrative approach identifies promising cold-active enzymes for potential application in the low-temperature biocatalysis industry.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148175708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Large-scale comparative genomics of chitin metabolism in extremely halophilic archaea from the Halobacteria class.","authors":"A S Tulenkov, A G Elcheninov, D Y Sorokin","doi":"10.1007/s00792-026-01432-7","DOIUrl":"10.1007/s00792-026-01432-7","url":null,"abstract":"<p><p>Chitin is the second most abundant polysaccharide and can serve as a carbon and nitrogen source for microorganisms in various ecosystems, including hypersaline environments. However, chitin metabolism in extremely halophilic archaea of the class Halobacteria has not been systematically analyzed, and the pathways of N-acetylglucosamine (GlcNAc) utilization in these organisms remain poorly understood. In this study, we performed a large-scale comparative genomic analysis of the class Halobacteria to assess prevalence and organization of genes, presumably involved in chitin utilization. Potential chitinolytic species are unevenly distributed across the class Halobacteria and tend to cluster within only 7 out of its 117 recognized genera. Glycoside hydrolases from GH18 and GH3 families were found as predominant endochitinases and β-hexosaminidases, respectively. Most putative chitinolytic haloarchaea lacked the genes involved in GlcNAc catabolism in bacteria and hyperthermophilic archaeon Thermococcus kodakaraensis. However, many of them harbor enzymes of pathways previously proposed for Natrarchaeobius and nanohaloarchaeon Ca. \"Nanohalobium constans\". Analysis of gene neighborhoods demonstrated a conserved organization of the gene clusters associated with chitin metabolism in some genomes, resembling the clusters previously described for Natrarchaeobius species. Overall, our results indicate that Halomicrobium, Natrarchaeobius, Natrialba, Saliphagus, Halocatena, Haladaptatus, and Salinarchaeum genera are enriched in species with chitinolytic potential.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148156099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Consortium of Sulfobacillus thermosulfidooxidans and Alicyclobacillus ferrooxydans facilitate pyrite bioleaching.","authors":"Chang Liu, Xiu-Tong Li, Yuqian Han, Wenxing Li, Yongqiang Gao, Chengying Jiang, Ying Liu, Yanning Zheng","doi":"10.1007/s00792-026-01429-2","DOIUrl":"10.1007/s00792-026-01429-2","url":null,"abstract":"<p><p>With the growing challenges of resource shortages and environmental pollution, bioleaching has attracted increasing attention for its high potential in processing refractory and low-grade ores. However, the slow growth rate and low biomass production of autotrophic bacteria commonly used in bioleaching limit their industrial application. Here, based on high-throughput sequencing analysis, which revealed a strong positive correlation between Sulfobacillus and Alicyclobacillus in mining environments, we developed a mixed-bacterial system composed of Sulfobacillus thermosulfidooxidans and Alicyclobacillus ferrooxydans to enhance the efficiency of bioleaching. The mixed-bacterial system achieved a pyrite leaching rate up to 91.14%, compared to 67.54% by S. thermosulfidooxidans and 17.63% by A. ferrooxydans. The improved leaching performance was attributed to the increased production of total extracellular polymeric substances (EPS), higher cell density and stronger redox capacity in the bioleaching solution. This study contributes to the development of a greener and more sustainable metallurgical industry.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147962535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative metagenomic analysis of microbial communities: unravelling microbial communities from the great Rann of Kachchh and coastal saltpans, Gujarat, India.","authors":"Rehnuma Ghori, Dineshram Ramadoss, Paul A Ramsland, Ewan W Blanch, Bharath Subramanyam Ammanabrolu","doi":"10.1007/s00792-026-01430-9","DOIUrl":"10.1007/s00792-026-01430-9","url":null,"abstract":"<p><p>Hypersaline environments exhibit extreme physiochemical conditions yet support diverse microbial communities. These communities are not only ecologically important but also possess substantial potential for biotechnological exploitation. In this study, we employed a comparative metagenomic approach to assess microbial diversity using two distinct methodologies: (1) direct DNA extraction from raw sediment, and (2) DNA extraction following halophilic enrichment in selective media. Sediment samples were collected from multiple sites and pooled together within the Rann of Kachchh and close-by saltpans and were analysed using 16S rRNA sequencing coupled with bioinformatics pipelines. The results revealed pronounced differences in microbial community composition between the two approaches. Raw sediment samples exhibited significantly higher alpha diversity, with dominant taxa including Halobacterota, Cyanobacteria, and Desulfobacterota, with a substantial proportion of unclassified genera. In contrast, enriched samples were dominated by fast-growing, culturable genera such as Halobacterium, Alkalibacillus, and Candidatus haloredivivus. Principal Coordinate Analysis (PCoA) of beta diversity demonstrated distinct clustering between raw and enriched communities, even within samples from the same sites, underscoring the selective bias introduced by enrichment procedures. These findings emphasise that the methodological choice strongly influences the observed microbial diversity. The aim of this study was to compare microbial community composition in raw hypersaline sediments and enrichment cultures using metagenomic sequencing, to evaluate how enrichment selectively favours specific halophilic taxa. This comparative approach allows identification of the microbial groups that rapidly proliferate under controlled hypersaline conditions, thereby complementing direct environmental sequencing. By integrating both direct and enrichment-based metagenomic approaches, a more comprehensive understanding of microbial community structure in hypersaline environments can be achieved.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147947965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteome-wide mapping of cysteine persulfidation in deep-sea hyperthermophilic archaea.","authors":"Ling Fu, Xuegong Li, Shaowei Liu, Yunhan Zhang, Jing Yang","doi":"10.1007/s00792-026-01428-3","DOIUrl":"10.1007/s00792-026-01428-3","url":null,"abstract":"<p><p>Protein persulfidation, a major post-translational modification mediated by the gaseous signaling molecule hydrogen sulfide (H₂S), regulates diverse physiological processes in eukaryotes and bacteria. However, its existence and functional roles in archaea, the third domain of life, remain entirely unexplored. Here, we investigate persulfidation in the deep-sea hyperthermophilic archaeon Thermococcus aciditolerans SY113, which thrives in sulfur rich hydrothermal vents and endogenously produces substantial H₂S. Our profiling not only delineated the unique reactivity landscape of this modification but also enabled quantitative analysis of its dynamic regulation by H₂S. A total of 204 persulfidation sites on 171 proteins were identified, of which over 65% were dynamically regulated by H₂S. Further functional analysis suggests that persulfidation represents an ancient and conserved regulatory mechanism in primordial life, including the regulation of catalytic activity and maintenance of protein conformation. Collectively, our findings provide a valuable dataset and a theoretical foundation for understanding the role of persulfidation in the physiological regulation of deep-sea hyperthermophilic archaea.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147812849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic and functional profiles of two Antarctic chitin-degrading Arthrobacter strains.","authors":"Yesenia M Santa-Cruz Vasquez, Luis Gabriel Cueva-Yesquen, Luiz Henrique Rosa, Alysson Wagner Fernandes Duarte, Valéria Maia de Oliveira","doi":"10.1007/s00792-026-01424-7","DOIUrl":"10.1007/s00792-026-01424-7","url":null,"abstract":"<p><p>Chitin is the second most abundant polysaccharide in nature and constitutes a key structural component in the cell wall of fungi and invertebrate exoskeletons. Chitinases produced by Antarctic organisms have demonstrated high catalytic efficiency, being promising tools for sustainable biotechnological processes. Therefore, the objective of this study was to identify the genes responsible for chitin degradation in the genomes of two Antarctic Arthrobacter strains, as well as to evaluate their biotechnological potential. Whole-genome sequencing followed by phylogenomic analysis revealed that both strains 492 and 285 belong to the species Arthrobacter psychrochitiniphilus. Genome assembly and annotation confirmed the genetic potential for chitinase production, showing that both bacteria possess the gene encoding type C chitinase (Chi C) from the GH18 family. Genomic comparative analysis revealed that they possess a total of eleven genes related to glycoside hydrolases (GH) and carbohydrate-binding modules (CBM), highlighting GH13 and GH65. Arthrobacter psychrochitiniphilus 492 was classified as psychrophilic, while A. psychrochitiniphilus 285 was classified as mesophilic-psychrotolerant. The enzyme production by A. psychrochitiniphilus 285 was 19.9 U/L, in 96 h at 15 °C, and the chitinase showed activity against the Aspergillus sp. series nigri CBMAI 1846, indicating promising potential for the formulation of bioinoculants and sustainable agriculture.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13106269/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147766923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cultivation and characterization of haloarchaea from Moroccan Atlantic solar salterns: insights into diversity and bioactive potential.","authors":"Imane Charroud, Naima Boum'handi, Mohamed Alouani, Altaf El Blidi, Yannick Fleury, Mohamed Jebbar","doi":"10.1007/s00792-026-01425-6","DOIUrl":"10.1007/s00792-026-01425-6","url":null,"abstract":"<p><p>This study provides the first culture-based inventory of haloarchaeal diversity in Moroccan Atlantic solar salterns (Oualidia and Khenifiss), using sediment samples collected across a gradient of moderate to high salinity (16.7–29.2% w/v) and slightly alkaline pH (7.4–7.5). A total of 69 representative isolates were phylogenetically assigned to nine genera within five families of the class Halobacteria. Both sites shared a core assemblage in which Halorubrum, Haloarcula, Haloferax, and Natrinema were the most frequently isolated taxa, whereas low-frequency genera (Halobacterium, Halogeometricum, Halococcus, Halomicrobium, and Halostagnicola) displayed differences in isolate recovery between sites, given the culture-dependent nature of the approach, no direct inference on in situ community structuring can be drawn. Several isolates display relatively low 16 S rRNA (< 98.65%) gene sequence similarity to validly published type strains and therefore constitute candidates for future genome-based taxonomic assessment. Standardized antagonism assays revealed inhibitory activity within and between sites, with Natrinema and Haloferax displaying the broadest inhibitory spectra. Collectively, these results provide new baseline data for Atlantic hypersaline sediments and highlight these environments as reservoirs of phylogenetically and functionally diverse extremophilic microorganisms.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147716469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fe-driven ROS mitigation in Leptolyngbya JSC-1: optimizing growth using response surface method.","authors":"Sikandar Khan, Maryam Akhoundian, Pengcheng Fu","doi":"10.1007/s00792-026-01427-4","DOIUrl":"10.1007/s00792-026-01427-4","url":null,"abstract":"<p><p>Leptolyngbya JSC-1 is a thermophilic and siderophilic cyanobacterium inhabiting iron-rich hot springs. Response surface method (RSM) is being reported for the first time for optimizing growth conditions of this thermophilic and siderophilic cyanobacterium. Using response surface quadratic model of Box-Behnken design, optimal culture conditions (A: temperature, 45 °C; B: Fe concentration, 42 µM; and C: light intensity, 2000 lx which is equivalent to 27 µmol photons m⁻² s⁻¹ intensity of cool white fluorescent lamp) were determined. The significant model terms were found to be B, AB, A², B², and C². The model R² value (coefficient of determination) was 0.939, suggesting that the fitted model could explain 93.9% of the total variation. Both the predicted response (OD₇₃₀ = 2.133) and experimental response (OD₇₃₀ = 2.1) were in proximity, suggested the appropriateness of the model and RSM. Moreover, an unusual inverse proportion was observed between the Fe concentration and ROS generation with the least ROS generation in JSC-1 grown with 42 µM Fe concentration. Hence, RSM allows evaluating the effects of multiple factors and their interactions on one or more response variables and is recommended to be used for multifactorial optimization studies.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147716486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extreme Arabian environments and their microbiomes: new frontiers for astrobiology and biosignature discovery.","authors":"Júnia Schultz, Paula M García-Martínez, Sharifah Altalhi, Nicholas Kontis, Alef Dos Santos, Alexandre Soares Rosado","doi":"10.1007/s00792-026-01426-5","DOIUrl":"10.1007/s00792-026-01426-5","url":null,"abstract":"<p><p>Astrobiology assesses the habitability of planetary bodies and the potential for extraterrestrial life. Analog environments on Earth serve as sites for studying extreme environments that resemble extraterrestrial conditions, aiding in validating life-detection methods, mission instrumentation, and biosignature preservation. These environments function as a source of model microorganisms and communities that define the habitability and biochemistry of such extraterrestrial environments. Well-known analog environments include the Atacama Desert (Chile) for space mission validation, the McMurdo Dry Valleys (Antarctica) for Mars analog studies, and Rio Tinto (Spain) for extreme acidic environments. Although significant research has been conducted on these sites, various alternative environments may also offer valuable opportunities for astrobiological studies. Saudi Arabia encompasses a variety of pristine (or with minimal anthropic influence) extreme environments with conditions analogous to extraterrestrial settings (e.g., deserts and salt flats as analogs to Mars, and terrestrial and marine volcanic fields as analogs to icy moons), yet their potential remains largely unexplored. Recent studies have identified a volcanic crater with sodium phosphates and chlorates that mimics Enceladus’s ocean chemistry, and researchers have cultured Halalkalibacterium halodurans strains with adaptations to survive these conditions, offering valuable biological models. Additionally, complex metabolic landscapes with implications for icy moon habitability have been observed in Red Sea systems, which could be employed as valuable natural laboratories in astrobiological research. Furthermore, these findings underscore the potential of the Saudi Arabian extremophilic microbiome for space-related research. This review explores the microbial diversity of extreme environments in Saudi Arabia, emphasizing their potential as new terrestrial analogs to Mars and icy moons and the role of their microbiomes as terrestrial proxies for extraterrestrial life.</p>","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"30 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13065566/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147638420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}